Progeny Analysis

Progeny analyses gene signatures and can score pathway activity of signalling pathways for a set of samples and also analyze the results from differential expression experiments.

Progeny results over all samples

The following plot shows the heatmap of Progeny score for gene expression normalized via DESeq2 for each sample.

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Per Pathway activity plots

Here we first visualize the distribution of pathway activities between the comparison given. A kruskal wallis test is run to test if samples originate from one or from multiple distributions.

Enrichment based off of differential gene expression analysis

Here we calculate the pathway enrichment based on the test statistic from DESeq2 to infer pathway changes between the comparison groups.

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

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## $VEGF

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## $WNT

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## $p53

DecoupleR

With the decoupleR prviding a new more flexible interface for Enrichment analyses. To retain comparisons with the original progeny method we reproduce most of the plots above but now use the newer decoupleR::run_wmean for inference in the progeny network.

Single sample mean plots using decoupler

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